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()))