def parse_inputs(parser, args):
if isinstance(args, list):
args, unknown = parser.parse_known_args()
if sys.argv[-2] == 'lbl' and sys.argv[-1] == 'stats':
print("Running in GUI mode")
title = 'Label Statistics'
vols = ['Input Volume', 'Registered Labels']
fields = ['Output file name', 'Sort (def = Mean)', 'Hemi', 'Label depth']
app = QApplication(sys.argv)
menu, linedits, labels = gui_opts.OptsMenu(title=title, vols=vols, fields=fields, helpfun=helpmsg())
menu.show()
app.exec_()
app.processEvents()
volstr = labels[vols[0]].text()
invol = str(volstr.split(":")[1]).lstrip()
lblsstr = labels[vols[1]].text()
lbls = str(lblsstr.split(":")[1]).lstrip()
outfile = 'clarity_label_statistics.csv' if not linedits[fields[0]].text() else str(linedits[fields[0]].text())
sort = 'Mean' if not linedits[fields[1]].text() else str(linedits[fields[1]].text())
hemi = 'Combined' if not linedits[fields[2]].text() else str(linedits[fields[2]].text())
label_depth = '' if not linedits[fields[3]].text() else str(linedits[fields[3]].text())
else:
print("\n running in script mode \n")
invol = args.invol
lbls = args.lbls
outfile = args.outfile
sort = args.sort
hemi = args.hemi if args.hemi is not None else "combined"
label_depth = args.depth if args.depth is not None else None
# check if pars given
assert isinstance(invol, str)
assert os.path.exists(invol), '%s does not exist ... please check path and rerun script' % invol
assert isinstance(lbls, str)
assert os.path.exists(lbls), '%s does not exist ... please check path and rerun script' % lbls
assert isinstance(outfile, str)
assert isinstance(sort, str)
return invol, lbls, outfile, sort, hemi, label_depth
def parse_inputs(parser, args):
if isinstance(args, list):
args, unknown = parser.parse_known_args()
if sys.argv[-2] == 'conv' and sys.argv[-1] == 'nii_tiff':
print("Running in GUI mode")
title = 'Nii to Tiff conversion'
dirs = ['Input Nii file']
fields = [
'Out nii name (def = clarity)', 'Up-sample ratio (def = 1)',
'Spline order (def = 3)'
]
app = QApplication(sys.argv)
menu, linedits, labels = gui_opts.OptsMenu(title=title,
dirs=dirs,
fields=fields,
helpfun=helpmsg())
menu.show()
app.exec_()
app.processEvents()
indirstr = labels[dirs[0]].text()
input = str(indirstr.split(":")[1]).lstrip()
assert os.path.exists(
input
), '%s does not exist ... please check path and rerun script' % input
# Initialize default params
outtiff = 'clarity.tif' if not linedits[fields[0]].text() else str(
linedits[fields[0]].text())
u = 1 if not linedits[fields[1]].text() else int(
linedits[fields[1]].text())
s = 3 if not linedits[fields[2]].text() else int(
linedits[fields[1]].text())
else:
print("\n running in script mode")
# check if pars given
assert isinstance(args.input, str)
input = args.input
assert os.path.exists(
input
), '%s does not exist ... please check path and rerun script' % input
if args.outtiff is None:
outtiff = 'clarity.tif'
else:
assert isinstance(args.outtiff, str)
outtiff = args.outtiff
if args.up is None:
u = 1
print(
"\n Up-sample ratio not specified ... choosing default value of %d"
% u)
else:
assert isinstance(args.up, int)
u = args.up
if args.spline is None:
s = 3
print(
"\n Spline order not specified ... choosing default value of %d"
% s)
else:
assert isinstance(args.spline, int)
s = args.spline
return input, outtiff, u, s
def parse_inputs(parser, args):
if isinstance(args, list):
args, unknown = parser.parse_known_args()
if sys.argv[-2] == 'conv' and sys.argv[-1] == 'tiff_nii':
print("Running in GUI mode")
title = 'Tiff to Nii conversion'
dirs = ['Input tiff folder']
fields = ['Output dir (def = working dir)', 'Out nii name (def = clarity)', 'Downsample ratio (def = 5)',
'chan # (def = 1)', 'chan prefix','Out chan name (def = eyfp)', 'Resolution (x,y) (def = 5 "um")',
'Thickness (z) (def = 5 "um")','center (def = 0,0,0)', 'Downsample in z (def = 1)',
'Prev Downsampling (def = 1 -> not downsampled)']
# field_names = ['outnii', 'd', 'chann', 'chanp', 'chan', 'vx', 'vz', 'cent', 'downz', 'pd']
app = QApplication(sys.argv)
menu, linedits, labels = gui_opts.OptsMenu(title=title, dirs=dirs, fields=fields, helpfun=helpmsg())
menu.show()
app.exec_()
app.processEvents()
indirstr = labels[dirs[0]].text()
indir = str(indirstr.split(":")[1]).lstrip()
assert os.path.exists(indir), '%s does not exist ... please check path and rerun script' % indir
# Initialize default params
work_dir = os.path.abspath(os.getcwd()) if not linedits[fields[0]].text() else str(linedits[fields[0]].text())
outnii = 'clarity' if not linedits[fields[1]].text() else str(linedits[fields[1]].text())
# assert isinstance(outnii, str), '-outnii not a string'
d = 5 if not linedits[fields[2]].text() else int(linedits[fields[2]].text())
# assert isinstance(d, int), '-d not a integer'
chann = 0 if not linedits[fields[3]].text() else int(linedits[fields[3]].text())
# assert isinstance(chann, int), '-chann not a integer'
chanp = None if not linedits[fields[4]].text() else str(linedits[fields[4]].text())
chan = 'eyfp' if not linedits[fields[5]].text() else str(linedits[fields[5]].text())
vx = 5 if not linedits[fields[6]].text() else float(linedits[fields[6]].text())
vz = 5 if not linedits[fields[7]].text() else float(linedits[fields[7]].text())
cent = [0, 0, 0] if not linedits[fields[8]].text() else linedits[fields[8]].text()
downz = 1 if not linedits[fields[9]].text() else int(linedits[fields[9]].text())
pd = 1 if not linedits[fields[10]].text() else int(linedits[fields[10]].text())
else:
print("\n running in script mode")
# check if pars given
assert isinstance(args.folder, str)
indir = args.folder
assert os.path.exists(indir), '%s does not exist ... please check path and rerun script' % indir
work_dir = args.work_dir
if args.outnii is None:
outnii = 'clarity'
else:
assert isinstance(args.outnii, str)
outnii = args.outnii
if args.down is None:
d = 5
print("\n down-sample ratio not specified ... choosing default value of %d" % d)
else:
assert isinstance(args.down, int)
d = args.down
if args.channum is None:
chann = 0
print("\n channel # not specified ... choosing default value of %d" % chann)
else:
assert isinstance(args.channum, int)
chann = args.channum
if args.chanprefix is None:
sys.exit('-cp (channel prefix) not specified ')
chanp = args.chanprefix if args.chanprefix is not None else None
if args.channame is None:
chan = 'eyfp'
print("\n channel name not specified ... choosing default value of %s" % chan)
else:
assert isinstance(args.channame, str)
chan = args.channame
if args.resx is None:
vx = 5
else:
vx = args.resx
if args.resz is None:
vz = 5
else:
vz = args.resz
if args.center is None:
cent = [0, 0, 0]
else:
cent = args.center
if args.downzdim is None:
downz = 1
else:
downz = args.downzdim
if args.prevdown is None:
pd = 1
else:
pd = args.prevdown
# make res in um
vx /= float(1000) # in um
vz /= float(1000)
return indir, work_dir, outnii, d, chann, chanp, chan, vx, vz, cent, downz, pd