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refactor: write_ome_metadata
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@calvinchai
calvinchai committed Nov 15, 2024
1 parent eb88d93 commit fd7e092
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Showing 2 changed files with 57 additions and 60 deletions.
91 changes: 47 additions & 44 deletions linc_convert/modalities/psoct/single_volume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@

from linc_convert.modalities.psoct.cli import psoct
from linc_convert.modalities.psoct.utils import make_json, generate_pyramid, \
niftizarr_write_header
niftizarr_write_header, write_ome_metadata
from linc_convert.utils.math import ceildiv
from linc_convert.utils.orientation import orientation_to_affine, center_affine
from linc_convert.utils.unit import to_ome_unit, to_nifti_unit
Expand Down Expand Up @@ -179,49 +179,7 @@ def convert(
print("Write metadata")
print(unit)
ome_unit = to_ome_unit(unit)
multiscales = [
{
"version": "0.4",
"axes": [
{"name": "z", "type": "space", "unit": ome_unit},
{"name": "y", "type": "space", "unit": ome_unit},
{"name": "x", "type": "space", "unit": ome_unit},
],
"datasets": [],
"type": ("2x2x2" if no_pool is None else "2x2") + "mean window",
"name": "",
}
]

for n in range(nblevels):
multiscales[0]["datasets"].append({})
level = multiscales[0]["datasets"][-1]
level["path"] = str(n)

# With a moving window, the scaling factor is exactly 2, and
# the edges of the top-left voxel are aligned
level["coordinateTransformations"] = [
{
"type": "scale",
"scale": [
(1 if no_pool == 0 else 2 ** n) * vx[0],
(1 if no_pool == 1 else 2 ** n) * vx[1],
(1 if no_pool == 2 else 2 ** n) * vx[2],
],
},
{
"type": "translation",
"translation": [
(0 if no_pool == 0 else (2 ** n - 1)) * vx[0] * 0.5,
(0 if no_pool == 1 else (2 ** n - 1)) * vx[1] * 0.5,
(0 if no_pool == 2 else (2 ** n - 1)) * vx[2] * 0.5,
],
},
]
multiscales[0]["coordinateTransformations"] = [
{"scale": [1.0] * 3, "type": "scale"}
]
omz.attrs["multiscales"] = multiscales
write_ome_metadata(omz, no_pool=no_pool, space_unit=ome_unit, space_scale=vx, multiscales_type=("2x2x2" if no_pool is None else "2x2") + "mean window")

if not nii:
print("done.")
Expand Down Expand Up @@ -256,6 +214,51 @@ def convert(
# print("done.")


# def write_ome_metadata(nblevels, no_pool, ome_unit, omz, vx):
# multiscales = [
# {
# "version": "0.4",
# "axes": [
# {"name": "z", "type": "space", "unit": ome_unit},
# {"name": "y", "type": "space", "unit": ome_unit},
# {"name": "x", "type": "space", "unit": ome_unit},
# ],
# "datasets": [],
# "type": ("2x2x2" if no_pool is None else "2x2") + "mean window",
# "name": "",
# }
# ]
# for n in range(nblevels):
# multiscales[0]["datasets"].append({})
# level = multiscales[0]["datasets"][-1]
# level["path"] = str(n)
#
# # With a moving window, the scaling factor is exactly 2, and
# # the edges of the top-left voxel are aligned
# level["coordinateTransformations"] = [
# {
# "type": "scale",
# "scale": [
# (1 if no_pool == 0 else 2 ** n) * vx[0],
# (1 if no_pool == 1 else 2 ** n) * vx[1],
# (1 if no_pool == 2 else 2 ** n) * vx[2],
# ],
# },
# {
# "type": "translation",
# "translation": [
# (0 if no_pool == 0 else (2 ** n - 1)) * vx[0] * 0.5,
# (0 if no_pool == 1 else (2 ** n - 1)) * vx[1] * 0.5,
# (0 if no_pool == 2 else (2 ** n - 1)) * vx[2] * 0.5,
# ],
# },
# ]
# multiscales[0]["coordinateTransformations"] = [
# {"scale": [1.0] * 3, "type": "scale"}
# ]
# omz.attrs["multiscales"] = multiscales


@contextmanager
def mapmat(fname, key=None):
"""Load or memory-map an array stored in a .mat file"""
Expand Down
26 changes: 10 additions & 16 deletions linc_convert/modalities/psoct/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,7 @@ def generate_pyramid(


def write_ome_metadata(
path: str | os.PathLike,
omz,
axes: list[str],
space_scale: float | list[float] = 1,
time_scale: float = 1,
Expand All @@ -267,6 +267,8 @@ def write_ome_metadata(
name: str = "",
pyramid_aligns: str | int | list[str | int] = 2,
levels: int | None = None,
no_pool: int | None = None,
multiscales_type : str = ""
) -> None:
"""
Write OME metadata into Zarr.
Expand Down Expand Up @@ -298,25 +300,19 @@ def write_ome_metadata(
"""

# Detect zarr version

# Read shape at each pyramid level
zname = ".zarray"
shapes = []
level = 0
while True:
if levels is not None and level > levels:
break

zpath = path / str(level) / zname
if not zpath.exists():
if str(level) not in omz.keys():
levels = level
break

level += 1
with zpath.open("rb") as f:
zarray = json.load(f)
shapes += [zarray["shape"]]
shapes += omz[str(level)].shape

axis_to_type = {
"x": "space",
Expand Down Expand Up @@ -370,7 +366,7 @@ def write_ome_metadata(
for axis in axes
],
"datasets": [],
"type": "median window " + "x".join(["2"] * sdim),
"type": "median window " + "x".join(["2"] * sdim) if not multiscales_type else multiscales_type,
"name": name,
}
]
Expand All @@ -391,6 +387,7 @@ def write_ome_metadata(
else ((shape0[bdim + i] - 1) / (shape[bdim + i] - 1))
)
* space_scale[i]
if i != no_pool else space_scale[i]
for i in range(sdim)
]
translation = [0] * bdim + [
Expand All @@ -403,6 +400,7 @@ def write_ome_metadata(
)
* 0.5
* space_scale[i]
if i != no_pool else 0
for i in range(sdim)
]

Expand All @@ -417,18 +415,14 @@ def write_ome_metadata(
},
]

scale = [1] * ndim
scale = [1.0] * ndim
if "t" in axes:
scale[axes.index("t")] = time_scale
multiscales[0]["coordinateTransformations"] = [{"scale": scale, "type": "scale"}]


multiscales[0]["version"] = "0.4"
with (path / ".zgroup").open("wt") as f:
json.dump({"zarr_format": 2}, f, indent=4)
with (path / ".zattrs").open("wt") as f:
json.dump({"multiscales": multiscales}, f, indent=4)

omz.attrs["multiscales"] = multiscales

def niftizarr_write_header(
omz,
Expand Down

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