def test_no_rootdir(self):
inpath = self.tempdir / 'foo/bar'
inpath.mkdir(parents=True)
res = utils.get_rootdir(inpath)
self.assertIsNone(res)
def test_gets_rootdir_from_channeldir(self):
rootdir = self.tempdir / 'foo/bar/2017-02-12'
rootdir.mkdir(parents=True)
inpath = rootdir / 'EGFP/'
res = utils.get_rootdir(inpath)
self.assertEqual(res, rootdir)
def test_gets_rootdir_from_imagefile(self):
rootdir = self.tempdir / 'foo/bar/2017-02-12'
rootdir.mkdir(parents=True)
inpath = rootdir / 'EGFP/s04-bees/foo-s04t003.tif'
res = utils.get_rootdir(inpath)
self.assertEqual(res, rootdir)
def test_ignores_non_existant_rootdir(self):
rootdir = self.tempdir / 'foo/bar/2017-02-12'
self.assertFalse(rootdir.is_dir())
inpath = rootdir / 'EGFP/'
res = utils.get_rootdir(inpath)
self.assertIsNone(res)
def test_ignores_weird_rootdir(self):
rootdir = self.tempdir / 'foo/bar/2017-02-12-bees'
rootdir.mkdir(parents=True)
inpath = rootdir / 'EGFP/'
res = utils.get_rootdir(inpath)
self.assertIsNone(res)
def test_gets_rootdir_from_imagefile_config_file(self):
rootdir = self.tempdir / 'foo/bar/baz'
rootdir.mkdir(parents=True)
(rootdir / 'deep_tracking.ini').touch()
inpath = rootdir / 'EGFP/s04-bees/foo-s04t003.tif'
res = utils.get_rootdir(inpath)
self.assertEqual(res, rootdir)
def get_names_for_plots(image_file: pathlib.Path,
plotdir: Optional[pathlib.Path] = None):
""" Get the names for the plotfile
:param Path image_file:
The image to evaluate
:param Path plotdir:
The directory to save plots to
:returns:
A tuple of plotfile, pointfile, response_file
"""
if plotdir is None:
rootdir = get_rootdir(image_file)
plotrel = image_file.relative_to(rootdir)
plotdir = rootdir / 'SingleCell' / plotrel.parent
plotfile = plotdir / (image_file.stem + '.png')
response_file = plotdir / (image_file.stem + '_resp.png')
pointfile = plotdir / (image_file.stem + '.csv')
return plotfile, pointfile, response_file
def test_gets_rootdir_from_rootdir(self):
inpath = self.tempdir / 'foo/bar/2017-02-12'
inpath.mkdir(parents=True)
res = utils.get_rootdir(inpath)
self.assertEqual(res, inpath)