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Add resolution level to data access #6

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merged 4 commits into from
Dec 6, 2023
Merged

Add resolution level to data access #6

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f022245
Add resolution level to data access
SeanLeRoy Dec 4, 2023
55af123
Try using multiscales array
SeanLeRoy Dec 4, 2023
132022a
Use index of datasets as resolution levels; map to path in data access
SeanLeRoy Dec 5, 2023
829eba0
Lint fix
SeanLeRoy Dec 6, 2023
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100 changes: 54 additions & 46 deletions bioio_ome_zarr/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,7 +69,6 @@ def __init__(

self._zarr = ZarrReader(parse_url(self._path, mode="r")).zarr
self._physical_pixel_sizes: Optional[types.PhysicalPixelSizes] = None
self._multiresolution_level = 0
self._channel_names: Optional[List[str]] = None

@staticmethod
Expand Down Expand Up @@ -99,14 +98,27 @@ def scenes(self) -> Tuple[str, ...]:
)
return self._scenes

@property
def resolution_levels(self) -> Tuple[int, ...]:
"""
Returns
-------
resolution_levels: Tuple[str, ...]
Return the available resolution levels for the current scene.
By default these are ordered from highest resolution to lowest
resolution.
"""
return tuple(rl for rl in range(len(self._zarr.root_attrs["multiscales"][self.current_scene_index]["datasets"])))

def _read_delayed(self) -> xr.DataArray:
return self._xarr_format(delayed=True)

def _read_immediate(self) -> xr.DataArray:
return self._xarr_format(delayed=False)

def _xarr_format(self, delayed: bool) -> xr.DataArray:
image_data = self._zarr.load(str(self.current_scene_index))
data_path = self._zarr.root_attrs["multiscales"][self.current_scene_index]["datasets"][self.current_resolution_level]["path"]
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Nit: maybe check that the level is valid before indexing into datasets here?

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Hmm do you think that is necessary with set_current_resolution_level() checking to see if it is valid at set time?

image_data = self._zarr.load(data_path)

axes = self._zarr.root_attrs["multiscales"][self.current_scene_index].get(
"axes"
Expand Down Expand Up @@ -139,11 +151,8 @@ def physical_pixel_sizes(self) -> types.PhysicalPixelSizes:
"""Return the physical pixel sizes of the image."""
if self._physical_pixel_sizes is None:
try:
z_size, y_size, x_size = Reader._get_pixel_size(
self._zarr,
z_size, y_size, x_size = self._get_pixel_size(
list(self.dims.order),
self._current_scene_index,
self._multiresolution_level,
)
except Exception as e:
warnings.warn(f"Could not parse zarr pixel size: {e}")
Expand All @@ -154,58 +163,23 @@ def physical_pixel_sizes(self) -> types.PhysicalPixelSizes:
)
return self._physical_pixel_sizes

@property
def channel_names(self) -> Optional[List[str]]:
if self._channel_names is None:
try:
self._channel_names = [
str(channel["label"])
for channel in self._zarr.root_attrs["omero"]["channels"]
]
except KeyError:
self._channel_names = super().channel_names
return self._channel_names

@staticmethod
def _get_coords(
dims: List[str],
shape: Tuple[int, ...],
scene: str,
channel_names: Optional[List[str]],
) -> Dict[str, Any]:
coords: Dict[str, Any] = {}

# Use dims for coord determination
if dimensions.DimensionNames.Channel in dims:
# Generate channel names if no existing channel names
if channel_names is None:
coords[dimensions.DimensionNames.Channel] = [
metadata_utils.generate_ome_channel_id(image_id=scene, channel_id=i)
for i in range(shape[dims.index(dimensions.DimensionNames.Channel)])
]
else:
coords[dimensions.DimensionNames.Channel] = channel_names

return coords

@staticmethod
def _get_pixel_size(
reader: ZarrReader, dims: List[str], series_index: int, resolution_index: int
self, dims: List[str],
) -> Tuple[Optional[float], Optional[float], Optional[float]]:
# OmeZarr file may contain an additional set of "coordinateTransformations"
# these coefficents are applied to all resolution levels.
if (
"coordinateTransformations"
in reader.root_attrs["multiscales"][series_index]
in self._zarr.root_attrs["multiscales"][self.current_scene_index]
):
universal_res_consts = reader.root_attrs["multiscales"][series_index][
universal_res_consts = self._zarr.root_attrs["multiscales"][self.current_scene_index][
"coordinateTransformations"
][0]["scale"]
else:
universal_res_consts = [1.0 for _ in range(len(dims))]

coord_transform = reader.root_attrs["multiscales"][series_index]["datasets"][
resolution_index
coord_transform = self._zarr.root_attrs["multiscales"][self.current_scene_index]["datasets"][
self.current_resolution_level
]["coordinateTransformations"]

spatial_coeffs = {}
Expand All @@ -229,3 +203,37 @@ def _get_pixel_size(
spatial_coeffs[dimensions.DimensionNames.SpatialY],
spatial_coeffs[dimensions.DimensionNames.SpatialX],
)

@property
def channel_names(self) -> Optional[List[str]]:
if self._channel_names is None:
try:
self._channel_names = [
str(channel["label"])
for channel in self._zarr.root_attrs["omero"]["channels"]
]
except KeyError:
self._channel_names = super().channel_names
return self._channel_names

@staticmethod
def _get_coords(
dims: List[str],
shape: Tuple[int, ...],
scene: str,
channel_names: Optional[List[str]],
) -> Dict[str, Any]:
coords: Dict[str, Any] = {}

# Use dims for coord determination
if dimensions.DimensionNames.Channel in dims:
# Generate channel names if no existing channel names
if channel_names is None:
coords[dimensions.DimensionNames.Channel] = [
metadata_utils.generate_ome_channel_id(image_id=scene, channel_id=i)
for i in range(shape[dims.index(dimensions.DimensionNames.Channel)])
]
else:
coords[dimensions.DimensionNames.Channel] = channel_names

return coords
35 changes: 29 additions & 6 deletions bioio_ome_zarr/tests/test_reader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
"filename, "
"set_scene, "
"expected_scenes, "
"set_resolution_level, "
"expected_resolution_levels, "
"expected_shape, "
"expected_dtype, "
"expected_dims_order, "
Expand All @@ -28,35 +30,43 @@
None,
None,
None,
None,
None,
marks=pytest.mark.xfail(raises=exceptions.UnsupportedFileFormatError),
),
# General Zarr
(
"s1_t1_c1_z1_Image_0.zarr",
"s1_t1_c1_z1",
("s1_t1_c1_z1",),
2,
(0, 1, 2, 3),
(1, 1, 1, 7548, 7549),
np.uint8,
dimensions.DEFAULT_DIMENSION_ORDER,
["Channel:0:0"],
(1.0, 264.5833333333333, 264.5833333333333),
(1.0, 1058.3333333333333, 1058.3333333333333),
),
# Complex General Zarr
(
"s1_t7_c4_z3_Image_0.zarr",
"s1_t7_c4_z3_Image_0",
("s1_t7_c4_z3_Image_0",),
3,
(0, 1, 2, 3),
(7, 4, 3, 1200, 1800),
np.uint16,
dimensions.DEFAULT_DIMENSION_ORDER,
["C:0", "C:1", "C:2", "C:3"],
(1.0, 1.0, 1.0),
(1.0, 8.0, 8.0),
),
# Test Resolution Constant
(
"resolution_constant_zyx.zarr",
"resolution_constant_zyx",
("resolution_constant_zyx",),
2,
(0, 1, 2, 3),
(2, 4, 4),
np.int64,
(
Expand All @@ -65,13 +75,15 @@
+ dimensions.DimensionNames.SpatialX
),
["Channel:0"],
(0.1, 0.1, 0.1),
(0.1, 0.4, 0.4),
),
# Test TYX
(
"dimension_handling_tyx.zarr",
"dimension_handling_tyx",
("dimension_handling_tyx",),
1,
(0, 1, 2, 3),
(2, 4, 4),
np.int64,
(
Expand All @@ -80,13 +92,15 @@
+ dimensions.DimensionNames.SpatialX
),
["Channel:0"],
(None, 1.0, 1.0),
(None, 2.0, 2.0),
),
# Test ZYX
(
"dimension_handling_zyx.zarr",
"dimension_handling_zyx",
("dimension_handling_zyx",),
1,
(0, 1, 2, 3),
(2, 4, 4),
np.int64,
(
Expand All @@ -95,13 +109,15 @@
+ dimensions.DimensionNames.SpatialX
),
["Channel:0"],
(1.0, 1.0, 1.0),
(1.0, 2.0, 2.0),
),
# Test TZYX
(
"dimension_handling_tzyx.zarr",
"dimension_handling_tzyx",
("dimension_handling_tzyx",),
0,
(0, 1, 2, 3),
(2, 2, 4, 4),
np.int64,
(
Expand All @@ -117,6 +133,8 @@
"absent_metadata_dims_zyx.zarr",
"absent_metadata_dims_zyx",
("absent_metadata_dims_zyx",),
3,
(0, 1, 2, 3),
(2, 4, 4),
np.int64,
(
Expand All @@ -125,14 +143,16 @@
+ dimensions.DimensionNames.SpatialX
),
["Channel:0"],
(1.0, 1.0, 1.0),
(1.0, 8.0, 8.0),
),
],
)
def test_ome_zarr_reader(
filename: str,
set_scene: str,
set_resolution_level: int,
expected_scenes: Tuple[str, ...],
expected_resolution_levels: Tuple[int, ...],
expected_shape: Tuple[int, ...],
expected_dtype: np.dtype,
expected_dims_order: str,
Expand All @@ -147,8 +167,11 @@ def test_ome_zarr_reader(
ImageContainer=Reader,
image=uri,
set_scene=set_scene,
set_resolution_level=set_resolution_level,
expected_scenes=expected_scenes,
expected_current_scene=set_scene,
expected_resolution_levels=expected_resolution_levels,
expected_current_resolution_level=set_resolution_level,
expected_shape=expected_shape,
expected_dtype=expected_dtype,
expected_dims_order=expected_dims_order,
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ classifiers = [
]
dynamic = ["version"]
dependencies = [
"bioio-base>=0.2.0",
"bioio-base>=1.0.0",
"fsspec>=2022.8.0",
"ome-zarr>=0.8.0",
"xarray>=0.16.1",
Expand Down
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