def test_group_can_select_channel_nested(self):
tempdir = self.tempdir
d1 = tempdir / 'TL Brightfield' / 's04'
d2 = tempdir / 'TL Brightfield' / 's03'
d3 = tempdir / 'mCherry' / 's04'
d4 = tempdir / 'mCherry' / 's05'
d1.mkdir(parents=True)
d2.mkdir(parents=True)
d3.mkdir(parents=True)
d4.mkdir(parents=True)
f1 = d1 / 'TL Brightfield-s04t045.tif'
f2 = d2 / 'TL Brightfield-s03t045.tif'
f3 = d3 / 'mCherry-s04t046.tif'
f4 = d4 / 'mCherry-s05t046.tif'
f1.touch()
f2.touch()
f3.touch()
f4.touch()
res = utils.group_image_files(tempdir, mode='nested', channel='brightfield')
exp = utils.TileGroup()
exp.extend([f1, f2])
self.assertEqual(res, exp)
res = utils.group_image_files(tempdir, mode='nested', channel='mcherry')
exp = utils.TileGroup()
exp.extend([f3, f4])
self.assertEqual(res, exp)
def test_group_single_tile_multi_channel_flat(self):
tempdir = self.tempdir
f1 = tempdir / 'TL Brightfield-s04t045.tif'
f2 = tempdir / 'mCherry-s04t046.tif'
f1.touch()
f2.touch()
res = utils.group_image_files(tempdir, mode='flat')
exp = utils.TileGroup()
exp.extend([f1, f2])
self.assertEqual(res, exp)
def test_group_can_select_channel_flat(self):
tempdir = self.tempdir
f1 = tempdir / 'TL Brightfield-s04t045.tif'
f2 = tempdir / 'TL Brightfield-s03t045.tif'
f3 = tempdir / 'mCherry-s04t046.tif'
f4 = tempdir / 'mCherry-s05t046.tif'
f1.touch()
f2.touch()
f3.touch()
f4.touch()
res = utils.group_image_files(tempdir, mode='flat', channel='brightfield')
exp = utils.TileGroup()
exp.extend([f1, f2])
self.assertEqual(res, exp)
res = utils.group_image_files(tempdir, mode='flat', channel='mcherry')
exp = utils.TileGroup()
exp.extend([f3, f4])
self.assertEqual(res, exp)
def test_group_single_tile_single_channel_nested(self):
tempdir = self.tempdir
d1 = tempdir / 'TL Brightfield' / 's04'
d1.mkdir(parents=True)
f1 = d1 / 'TL Brightfield-s04t045.tif'
f2 = d1 / 'TL Brightfield-s04t046.tif'
f1.touch()
f2.touch()
res = utils.group_image_files(tempdir, mode='nested')
exp = utils.TileGroup()
exp.extend([f1, f2])
self.assertEqual(res, exp)