def test_czi_read_mc_std_preprocess():
image_fp = os.path.join(PRIVATE_DIR, "czi_4ch_16bit.czi")
preprocessing = std_prepro()
ri = reg_image_loader(image_fp, 1, preprocessing=preprocessing)
ri.read_reg_image()
assert ri.image.GetNumberOfComponentsPerPixel() == 1
assert ri.image.GetPixelID() == 1
def __init__(
self,
image_fp,
image_res,
mask=None,
pre_reg_transforms=None,
preprocessing=None,
channel_names=None,
channel_colors=None,
):
self.image_filepath = image_fp
self.image_res = image_res
self.image = None
self.czi = CziRegImageReader(self.image_filepath)
self.reader = "czi"
(
self.ch_dim_idx,
self.y_dim_idx,
self.x_dim_idx,
self.im_dims,
self.im_dtype,
) = self._get_image_info()
self.im_dims = tuple(self.im_dims)
self.is_rgb = guess_rgb(self.im_dims)
self.n_ch = self.im_dims[2] if self.is_rgb else self.im_dims[0]
self.mask = self.read_mask(mask)
if preprocessing is None:
self.preprocessing = std_prepro()
else:
self.preprocessing = std_prepro()
self.preprocessing.update(preprocessing)
self.pre_reg_transforms = pre_reg_transforms
self.channel_names = channel_names
self.channel_colors = channel_colors
self.original_size_transform = None
def __init__(
self,
image_fp,
image_res,
mask=None,
pre_reg_transforms=None,
preprocessing=None,
channel_names=None,
channel_colors=None,
):
self.image_filepath = image_fp
self.image_res = image_res
self.image = None
self.tf = TiffFile(self.image_filepath)
self.reader = "tifffile"
self.ome_metadata = xml2dict(self.tf.ome_metadata)
(
self.im_dims,
self.im_dtype,
) = self._get_image_info()
self.im_dims = tuple(self.im_dims)
# self.n_ch = self.im_dims[2] if self.is_rgb else self.im_dims[0]
self.mask = self.read_mask(mask)
if preprocessing is None:
self.preprocessing = std_prepro()
else:
self.preprocessing = std_prepro()
self.preprocessing.update(preprocessing)
self.pre_reg_transforms = pre_reg_transforms
self.channel_names = channel_names
self.channel_colors = channel_colors
self.original_size_transform = None