def tf_get_largest_series(image_filepath):
"""
Determine largest series for .scn files by examining metadata
For other multi-series files, find the one with the most pixels
Parameters
----------
image_filepath: str
path to the image file
Returns
-------
largest_series:int
index of the largest series in the image data
"""
fp_ext = Path(image_filepath).suffix.lower()
tf_im = TiffFile(image_filepath)
if fp_ext == ".scn":
scn_meta = xml2dict(tf_im.scn_metadata)
image_meta = scn_meta.get("scn").get("collection").get("image")
largest_series = np.argmax([
im.get("scanSettings").get("objectiveSettings").get("objective")
for im in image_meta
])
else:
largest_series = np.argmax([
np.prod(np.asarray(series.shape), dtype=np.int64)
for series in tf_im.series
])
return largest_series
def convert_nd2_to_ome_tiff(path, outpath):
"""
Convert an nd2 file to an .ome.tif by saving each tile under a separate series.
Uses the BigTIFF format to write the new .ome.tiff file.
"""
path_to_nd2 = str(path)
omexml = get_editable_omexml(path_to_nd2)
limit = omexml.image_count
xml_dict = tifffile.xml2dict(omexml.to_xml())
with ND2Reader(path_to_nd2) as images:
print(images.sizes)
images.iter_axes = 'v'
images.bundle_axes = "zcyx"
with tifffile.TiffWriter(outpath, bigtiff=True) as tif:
for series, tile in enumerate(images):
# TODO: seems like, for some weird reason, the tiles are rotated incorrectly? Why?
# Maybe it has to do with the order of the bundle axes
rotated_tile = np.rot90(tile, k=1, axes=(2, 3))
series_metadata = xml_dict["OME"]["Image"][series]
tif.save(rotated_tile.astype(np.uint16),
contiguous=False,
metadata=series_metadata)
def ome_tifffile_to_arraylike(image_filepath):
ome_metadata = xml2dict(TiffFile(image_filepath).ome_metadata)
im_dims, im_dtype = get_tifffile_info(image_filepath)
largest_series_idx = tf_get_largest_series(image_filepath)
series_metadata = ome_metadata.get("OME").get("Image")
if isinstance(series_metadata, list):
series_metadata = series_metadata[largest_series_idx]
if isinstance(series_metadata.get("Pixels").get("Channel"), list):
samples_per_pixel = (series_metadata.get("Pixels").get("Channel")
[0].get("SamplesPerPixel"))
else:
samples_per_pixel = (series_metadata.get("Pixels").get("Channel").get(
"SamplesPerPixel"))
is_rgb = guess_rgb(im_dims)
image = zarr.open(
imread(image_filepath, aszarr=True, series=largest_series_idx))
if isinstance(image, zarr.Group):
image = image[0]
image = da.from_zarr(image)
if samples_per_pixel:
if is_rgb is False and samples_per_pixel >= 3:
image = image.transpose(1, 2, 0)
return image, image_filepath
def test_ome_save(tmp_path, bundle_test_dir, ome_xml, z_size):
data = np.zeros((z_size, 20, 20, 2), dtype=np.uint8)
image = Image(
data,
image_spacing=(27 * 10 ** -6, 6 * 10 ** -6, 6 * 10 ** -6),
axes_order="ZYXC",
channel_names=["a", "b"],
shift=(10, 9, 8),
name="Test",
)
ImageWriter.save(image, tmp_path / "test.tif")
with tifffile.TiffFile(tmp_path / "test.tif") as tiff:
assert tiff.is_ome
assert isinstance(tiff.ome_metadata, str)
meta_data = tifffile.xml2dict(tiff.ome_metadata)["OME"]["Image"]
assert "PhysicalSizeX" in meta_data["Pixels"]
assert meta_data["Pixels"]["PhysicalSizeX"] == 6
assert "PhysicalSizeXUnit" in meta_data["Pixels"]
assert meta_data["Pixels"]["PhysicalSizeXUnit"] == "µm"
assert len(meta_data["Pixels"]["Channel"]) == 2
assert meta_data["Pixels"]["Channel"][0]["Name"] == "a"
assert meta_data["Pixels"]["Channel"][1]["Name"] == "b"
assert meta_data["Name"] == "Test"
xml_file = etree.fromstring(tiff.ome_metadata.encode("utf8")) # nosec
ome_xml.assert_(xml_file)
read_image = TiffImageReader.read_image(tmp_path / "test.tif")
assert np.allclose(read_image.spacing, image.spacing)
assert np.allclose(read_image.shift, image.shift)
assert read_image.channel_names == ["a", "b"]
assert read_image.name == "Test"
def test_xml2dict():
sample_text = """
<level1>
<level2>3.5322</level2>
</level1>
"""
data = tifffile.xml2dict(sample_text)
assert math.isclose(data["level1"]["level2"], 3.5322)
def metadata(self, raw=False):
"""Read metadata from file and return as dict (default) or XML."""
if self.metadata_size <= 0:
return u'' if raw else None
fh = self._fh
with fh.lock:
fh.seek(self.data_offset - self.metadata_size)
metadata = fh.read(self.metadata_size)
if raw:
return unicode(metadata, 'utf-8')
try:
return xml2dict(metadata)['METADATA']
except Exception:
return unicode(metadata, 'utf-8')
def parse_dispim_meta(impath):
# parse TiffFile.ome_metadata to extract diSPIM info
with tf.TiffFile(impath) as t:
meta = t.ome_metadata
# tifffile version > 2019.2.22
if isinstance(meta, str):
meta = tf.xml2dict(meta)["OME"]
im0 = meta["Image"][0] if isinstance(meta["Image"],
list) else meta["Image"]
out = {"channels": [], "nS": len(meta["Image"])}
for x in "XYZCT":
out["n" + x] = im0["Pixels"]["Size" + x]
for x in "XYZ":
out["d" + x] = im0["Pixels"]["PhysicalSize" + x]
for chan in im0["Pixels"]["Channel"]:
out["channels"].append(chan["Name"])
out["dzRatio"] = out["dZ"] / out["dX"]
return out
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
def slice_ome_tiff(input_filepath,
output_filepath,
start,
end,
use_bigtiff=False):
"""
Build a new .ome.tiff with only the series that fall in the range start:end included (+ metadata).
"""
# TODO: Add an IndexError or whatever later
input_ome_tiff = tifffile.TiffFile(input_filepath)
xml = input_ome_tiff.ome_metadata
xml_dict = tifffile.xml2dict(xml)
print(input_filepath)
with tifffile.TiffWriter(output_filepath, bigtiff=use_bigtiff) as tif:
for index in range(start, end):
print(index)
tile = input_ome_tiff.series[index].asarray()
tile_metadata = xml_dict["OME"]["Image"][index]
tif.save(tile.astype(np.uint16),
contiguous=False,
metadata=tile_metadata)
def data(self, raw=True):
"""Read metadata from file and return as XML (default) or dict."""
self._fh.seek(self.xml_offset)
xml = self._fh.read(self.xml_size)
xml = xml.replace(b'\r\n', b'\n').replace(b'\r', b'\n') # ???
return unicode(xml, 'utf-8') if raw else xml2dict(xml)
def read_xml(fh, filesize, raw=True):
"""Read XML from file and return as unicode string (default) or dict."""
xml = stripnull(fh.read(filesize))
return unicode(xml, 'utf-8') if raw else xml2dict(xml)
def find_ome_magnification(ome_xml):
metadata = tifffile.xml2dict(ome_xml)