def savePkl(db,f):
pklPath = os.path.join(os.path.split(outputDir)[0],'pklFiles')
if not os.path.exists(pklPath): makeDir(pklPath)
fpath = os.path.join(pklPath,f)
ofile = open(fpath,'w')
pickle.dump(db,ofile)
ofile.close()
return True
def tempFunction():
sourceDir = '/home/jaggu/marcotte_project/boulgakov/microscope/2016-July/2016-07-21t/before_after'
destDir = os.path.join(sourceDir,'convertedImages')
makeDir(destDir)
all_subDir = [d for d in os.walk(sourceDir).next()[1] if not d.endswith('trace') ]
for subDir in all_subDir:
convertDir(subDir)
return True
def colocalizeImages(dateStamp, pathDir, destDir):
print dateStamp
print pathDir
print destDir
processed_dir = os.path.join(destDir, "colocalizePKL")
makeDir(processed_dir)
pklFname = os.path.join(processed_dir, dateStamp + '_colocalize.pkl')
ofile = open(pklFname, 'w')
subDir_colocal_dict = collections.defaultdict(list)
allSubDir = [
os.path.join(pathDir, d) for d in os.walk(pathDir).next()[1]
if d.startswith('16')
] #Dirty exception
for subDir in allSubDir:
print "Processing directory %s ..." % (subDir)
f = str()
allFile_pairs = list()
f = os.path.split(subDir)[1]
allPkl = [
os.path.join(subDir, f) for f in os.listdir(subDir)
if f.endswith('.pkl') and 'c1.tif.png' in f
]
for pklF in allPkl:
file_list = list()
suf = ".".join(pklF.split('.')[1:])
pre = pklF.split('.')[0]
if pre.endswith('c1'):
for nbr in range(1, 6):
f = pre[:-2] + 'c' + str(nbr) + '.' + suf
if os.path.isfile(f): file_list.append(f)
else:
file_couple = list(itertools.combinations(
file_list, 2))
allFile_pairs.append(file_couple)
break
else:
raise SystemExit("Need atleast two files to compare")
for subDir_list in allFile_pairs:
for f1, f2 in subDir_list:
colocal = Colocalize(f1, f2)
overlapPeaks = colocal.checkPosOverlap()
subDir_colocal_dict[subDir].append([
f1, f2, colocal.f1NbrPeaks, colocal.f2NbrPeaks,
len(overlapPeaks)
])
pickle.dump(subDir_colocal_dict, ofile)
return subDir_colocal_dict
def saveProjected(self,img,offsetDict,type='max',dest_dir=None,fname=None,level=1):
if not dest_dir:
dest_dir = os.path.split(self.imagesList[self.IDX])[0]
if not fname:
fname = '.'.join([self.imagesList[self.IDX][:-4],type+'_projection'])
target_dir = os.path.join(dest_dir,'projectionImages')
cfunc.makeDir(target_dir)
f_img_name = os.path.join(target_dir,fname+'.level_'+str(level)+'.image.tif')
f_offset_name = os.path.join(target_dir,fname+'.level_'+str(level)+'.offset_dict.pkl')
cv2.imwrite(f_img_name,img)
with open(f_offset_name,'wb') as ofile:
pickle.dump(offsetDict,ofile)
return f_img_name, f_offset_name
def colocalizeImages(dateStamp,pathDir,destDir):
print dateStamp
print pathDir
print destDir
processed_dir = os.path.join(destDir,"colocalizePKL")
makeDir(processed_dir)
pklFname = os.path.join(processed_dir,dateStamp + '_colocalize.pkl')
ofile = open(pklFname,'w')
subDir_colocal_dict = collections.defaultdict(list)
allSubDir = [os.path.join(pathDir,d) for d in os.walk(pathDir).next()[1] if d.startswith('16')] #Dirty exception
for subDir in allSubDir:
print "Processing directory %s ..."%(subDir)
f = str()
allFile_pairs = list()
f = os.path.split(subDir)[1]
allPkl = [os.path.join(subDir,f) for f in os.listdir(subDir) if
f.endswith('.pkl') and 'c1.tif.png' in f]
for pklF in allPkl:
file_list = list()
suf = ".".join(pklF.split('.')[1:])
pre = pklF.split('.')[0]
if pre.endswith('c1'):
for nbr in range( 1,6):
f = pre[:-2]+'c'+str(nbr)+'.'+suf
if os.path.isfile(f): file_list.append(f)
else:
file_couple = list(itertools.combinations(file_list,2))
allFile_pairs.append(file_couple)
break
else: raise SystemExit("Need atleast two files to compare")
for subDir_list in allFile_pairs:
for f1,f2 in subDir_list:
colocal = Colocalize(f1,f2)
overlapPeaks = colocal.checkPosOverlap()
subDir_colocal_dict[subDir].append([f1,f2,colocal.f1NbrPeaks,colocal.f2NbrPeaks,len(overlapPeaks)])
pickle.dump(subDir_colocal_dict,ofile)
return subDir_colocal_dict
destDir = os.path.join(
"/project/jagannath/projectfiles/singleMoleculeMicroscopy/dataAnalysis/microscope1",
monthStamp, dateStamp)
elif microscope is 2:
sourceDir = "/project/boulgakov/microscope2/jagannath/rawFiles"
pathDir = os.path.join(sourceDir, monthStamp, dateStamp)
destDir = os.path.join(
"/project/current/project2/jaggu/dataAnalysis/microscope2",
monthStamp, dateStamp)
elif microscope is 3:
sourceDir = "/project/boulgakov/microscope3/rawFiles/jagannath"
pathDir = os.path.join(sourceDir, monthStamp, dateStamp)
destDir = os.path.join(
"/project/current/project2/jaggu/dataAnalysis/microscope3",
monthStamp, dateStamp)
else:
raise SystemExit("Incorrect microscope number. Quiting ..")
makeDir(destDir)
t0 = time.clock()
if ARG == 'COLOCALIZE':
colocal_dict = colocalizeImages(dateStamp, pathDir, destDir)
writeToFile(colocal_dict, dateStamp, destDir)
t1 = time.clock()
print "Script - %s \t Completed in %s secs \t %s" % (
sys.argv, t1 - t0, time.strftime("%d %b %Y %H:%M:%S",
time.localtime()))
# pathDir = os.path.join(sourceDir,subDir)
microscope = 1
if microscope is 1:
sourceDir = "/project/boulgakov/microscope"
pathDir = os.path.join(sourceDir,monthStamp,dateStamp)
destDir = os.path.join("/project/jagannath/projectfiles/singleMoleculeMicroscopy/dataAnalysis/microscope1",monthStamp,dateStamp)
elif microscope is 2:
sourceDir = "/project/boulgakov/microscope2/jagannath/rawFiles"
pathDir = os.path.join(sourceDir,monthStamp,dateStamp)
destDir = os.path.join("/project/current/project2/jaggu/dataAnalysis/microscope2",monthStamp,dateStamp)
elif microscope is 3:
sourceDir = "/project/boulgakov/microscope3/rawFiles/jagannath"
pathDir = os.path.join(sourceDir,monthStamp,dateStamp)
destDir = os.path.join("/project/current/project2/jaggu/dataAnalysis/microscope3",monthStamp,dateStamp)
else:
raise SystemExit("Incorrect microscope number. Quiting ..")
makeDir(destDir)
t0 = time.clock()
if ARG == 'COLOCALIZE':
colocal_dict = colocalizeImages(dateStamp,pathDir,destDir)
writeToFile(colocal_dict,dateStamp,destDir)
t1 = time.clock()
print "Script - %s \t Completed in %s secs \t %s"%(sys.argv, t1-t0,
time.strftime("%d %b %Y %H:%M:%S",time.localtime()))
