def __init__(self, slide_path: str):
self.slide_path = slide_path
reader = CziFile(slide_path)
if not reader.is_mosaic():
raise NotImplementedError(
'This class has only been defined for mosaic czi files. '
'You should be able to simply convert the non-mosaic czi-file '
'into a format that can be opened with openslide.'
)
self.bboxes = np.array(reader.mosaic_scene_bounding_boxes())
self.data_mask = self._get_data_mask(self.bboxes)
self.shape = reader.read_mosaic_size()
self.dimensions = self.shape[2:]
self.region_mask = self._get_region_mask(self.shape)
def test_mosaic_subblock_rect(data_dir, fname, s_index, m_index, expected):
with open(data_dir / fname, 'rb') as fp:
czi = CziFile(czi_filename=fp)
data = czi.mosaic_scene_bounding_boxes(s_index)
assert data == expected
