def test_update_folder_info_from(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well._update_info_from(labeled_f0.info)
is_ok = [getattr(well, a) == getattr(labeled_f0.info, a)
for a in well._check_attrs]
self.assertTrue(all(is_ok))
def test_getitem(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(labeled_f0)
gotten = well[labeled_f0.info.focus]
self.assertIs(type(gotten), AnnotatedFocusFolder)
def test_collate_wells(self):
label = AnnotatedImage(INFO_F0, '1-cell')
data = AnnotatedImage(label.info, [0, 1, 2])
well_labeled = AnnotatedWellFolder.create_from(label)
well_data = AnnotatedWellFolder.create_from(data)
collated = well_labeled.collate_annotations_with(well_data)
well_labeled.update_with(data)
self.assertEqual(well_labeled, collated)
def test_update_with_when_empty(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(labeled_f0)
self.assertEqual(len(well), 1)
info_ok = [getattr(well, a) == getattr(labeled_f0.info, a)
for a in well._check_attrs]
self.assertTrue(all(info_ok))
type_ok = type(well[labeled_f0.info.focus]) == AnnotatedFocusFolder
self.assertTrue(type_ok)
def test_remove_recursively_when_image_is_not_in_wellfolder(self):
labeled1 = AnnotatedImage(INFO_F0, '1-cell')
labeled2 = AnnotatedImage(INFO_F0_2, '1-cell')
well = AnnotatedWellFolder.create_from(labeled1)
well.update_with(labeled2)
labeled_notin = AnnotatedImage(INFO_FP, '1-cell')
self.assertRaises(ValueError, well.remove, labeled_notin)
def test_add_entry_from_includes_in_dict(self):
well = AnnotatedWellFolder()
image1 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(image1)
image2 = AnnotatedImage(INFO_F0_2, '1-cell')
well._add_entry_from(image2)
self.assertTrue(well.contains_image(image2.info))
def test_iterate_over_images(self):
labeled1 = AnnotatedImage(INFO_F0, '1-cell')
labeled2 = AnnotatedImage(INFO_F0_2, '1-cell')
well = AnnotatedWellFolder.create_from(labeled1)
well.update_with(labeled2)
images = [i for i in well.iterate_over_images()]
self.assertEqual(len(images), 2)
self.assertIn(labeled1, images)
self.assertIn(labeled2, images)
def test_remove_recursively_when_image_is_in_wellfolder(self):
labeled1 = AnnotatedImage(INFO_F0, '1-cell')
labeled2 = AnnotatedImage(INFO_F0_2, '1-cell')
well = AnnotatedWellFolder.create_from(labeled1)
well.update_with(labeled2)
well.remove(labeled1, recursive=True)
# There should still be 1 focus:
self.assertEqual(len(well), 1)
# But the image should not be in the focus folder:
focus = [i for i in well][0]
self.assertTrue(labeled1 not in focus)
def test_does_update_with_if_same_well(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(labeled_f0)
labeled_fm_2 = AnnotatedImage(INFO_FM_2, '1-cell')
well.update_with(labeled_fm_2)
self.assertEqual(len(well), 2)
def test_does_update_with_if_same_focus(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(labeled_f0)
labeled_f0_2 = AnnotatedImage(INFO_F0_2, '1-cell')
well.update_with(labeled_f0_2)
# Then the length should be 1, since it should update the same
# dictionary!
self.assertEqual(len(well), 1)
def test_deprettify(self):
focus_value = 15
pretty = AnnotatedWellFolder._prettify(focus_value)
back = AnnotatedWellFolder._de_prettify(pretty)
self.assertEqual(back, focus_value)
def test_prettify(self):
focus_value = 15
correct = 'F15'
output = AnnotatedWellFolder._prettify(focus_value)
self.assertEqual(output, correct)
def test_does_not_update_with_if_different_well(self):
well = AnnotatedWellFolder()
labeled_f0 = AnnotatedImage(INFO_F0, '1-cell')
well.update_with(labeled_f0)
labeled_fp = AnnotatedImage(INFO_FP, '1-cell')
self.assertRaises(ValueError, well.update_with, labeled_fp)
def test_len_is_zero_on_init(self):
well = AnnotatedWellFolder()
self.assertEqual(len(well), 0)
def test_init_does_not_crash(self):
well = AnnotatedWellFolder()
self.assertTrue(well is not None)