def test_detect_dormat():
assert detect_format(os.path.join(DATADIR, 'di1.di')) == 'di'
assert detect_format(os.path.join(DATADIR, 'di2.di')) == 'di'
assert detect_format(os.path.join(DATADIR, 'example.ibw')) == 'ibw'
assert detect_format(os.path.join(DATADIR, 'example.opd')) == 'opd'
assert detect_format(os.path.join(DATADIR, 'example.x3p')) == 'x3p'
assert detect_format(os.path.join(DATADIR, 'example1.mat')) == 'mat'
assert detect_format(os.path.join(DATADIR, 'example.asc')) == 'xyz'
assert detect_format(
os.path.join(DATADIR, 'line_scan_1_minimal_spaces.asc')) == 'xyz'
assert detect_format(os.path.join(DATADIR, 'example-2d.npy')) == 'npy'
assert detect_format(os.path.join(DATADIR, 'surface.2048x2048.h5')) == 'h5'
def handle(self, *args, **options):
format_counts = { None: 0 }
num_cannot_openend = 0 # number of files which cannot be openend
topographies = Topography.objects.all()
if not options['all']:
topographies = topographies.filter(datafile_format__isnull=True)
num_topographies = topographies.count()
for topo in topographies:
if topo.datafile_format is None:
try:
datafile = topo.datafile
# Workaround such that module "SurfaceTopography" recognizes this a binary stream
if not hasattr(datafile, 'mode'):
datafile.mode = 'rb'
datafile_format = detect_format(datafile)
except CannotDetectFileFormat as exc:
msg = f"Could not detect format for topography id {topo.id}: "+str(exc)
self.stdout.write(self.style.WARNING(msg))
format_counts[None] += 1
continue
except Exception as exc:
msg = f"Could not open file for topography id {topo.id}: " + str(exc)
self.stdout.write(self.style.WARNING(msg))
num_cannot_openend += 1
continue
if not options['dry_run']:
topo.datafile_format = datafile_format
topo.save()
if datafile_format not in format_counts:
format_counts[datafile_format] = 1
else:
format_counts[datafile_format] += 1
self.stdout.write(self.style.SUCCESS(f"Processed {num_topographies} specified topographies."))
if num_cannot_openend == 0:
self.stdout.write(self.style.SUCCESS("All specified topography files can be opened."))
else:
self.stdout.write(self.style.ERROR("In total {} of {} topographies currently cannot be opened.".format(
num_cannot_openend, num_topographies)))
self.stdout.write(self.style.SUCCESS("Frequencies of topographies which could be opened:"))
for fmt, freq in format_counts.items():
self.stdout.write(self.style.SUCCESS(f" {fmt}: {freq}"))
if format_counts[None] == 0:
self.stdout.write(self.style.SUCCESS("All {} topography files which can be opened can also be loaded.".format(
num_topographies-num_cannot_openend)))
else:
self.stdout.write(self.style.WARNING("In total {} topographies currently can be opened, but not be loaded.".format(
format_counts[None])))
if options['dry_run']:
self.stdout.write(self.style.WARNING("This was a dry run, nothing has been changed."))
def test_detect_format_then_read(self):
self.assertEqual(
detect_format(
os.path.join(DATADIR, 'line_scan_1_minimal_spaces.asc')),
'xyz')
def test_detect_format_then_read(self):
f = open(os.path.join(DATADIR, 'example.ibw'), 'rb')
fmt = detect_format(f)
self.assertTrue(fmt, 'ibw')
open_topography(f, format=fmt).topography()
f.close()