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)