def writeLocations(srcDir,outfile,overwrite=True):
"""Extract the recording locations and write to a csv file"""
try:
if overwrite:
f = open(outfile,'w')
else:
f = open(outfile,'w+')
except IOError as e:
logger.error('Could not open file:{} for writing. {}'.format(outfile,e))
recordingCoords = psiSession.getImagingSessionInfo(srcDir)
csv_writer = csv.DictWriter(f,
delimiter=',',
fieldnames=recordingCoords[0].keys())
if overwrite:
csv_writer.writeheader()
for row in recordingCoords:
csv_writer.writerow(row)
f.close()
# check the outdir exists
if args.outDir:
try:
os.mkdir(args.outDir)
except OSError as e:
if e.errno == 17:
#already exists
pass
else:
logger.error('Failed to create output dir {}. {}'.format(args.outDir,e))
if args.outDir:
writeLocations(args.sourceDir,
os.path.join(args.outDir,'locations.csv'),
args.overwrite)
else:
print psiSession.getImagingSessionInfo(args.sourceDir)
#now align the files
recordings = psiSession.getRecordings(args.sourceDir)
#for recording in recordings[0]:
for recording in recordings:
alignSloFile(args.sourceDir,
recording,
args.outDir,
args.moveLocal,
args.writeStable,
args.writeFrames)