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Updated .zattrs file #18

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Updated .zattrs file #18

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cd18dab
Updated .zattrs file
Nov 12, 2024
4404499
style fixes by ruff
jingjingwu1225 Nov 12, 2024
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82 changes: 39 additions & 43 deletions linc_convert/modalities/df/multi_slice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -174,43 +174,41 @@ def convert(
x = floordiv(shape[-2] - subdat_size[-2], 2)
y = floordiv(shape[-1] - subdat_size[-1], 2)

if max_load is None or (shape[-2] < max_load and shape[-1] < max_load):
array[..., idx, x : x + subdat_size[1], y : y + subdat_size[2]] = (
subdat[...]
)

else:
ni = ceildiv(shape[-2], max_load)
nj = ceildiv(shape[-1], max_load)

for i in range(ni):
for j in range(nj):
print(f"\r{i+1}/{ni}, {j+1}/{nj}", end=" ")
start_x, end_x = (
i * max_load,
min((i + 1) * max_load, shape[-2]),
)
start_y, end_y = (
j * max_load,
min((j + 1) * max_load, shape[-1]),
)
if end_x <= x or end_y <= y:
continue

if start_x >= subdat_size[-2] or start_y >= subdat_size[-1]:
continue

array[
...,
idx,
x + start_x : x + min(end_x, subdat_size[-2]),
y + start_y : y + min(end_y, subdat_size[-1]),
] = subdat[
...,
start_x : min((i + 1) * max_load, subdat_size[-2]),
start_y : min((j + 1) * max_load, subdat_size[-1]),
]
print("")
for channel in range(3):
if max_load is None or (
subdat_size[-2] < max_load and subdat_size[-1] < max_load
):
array[
channel, idx, x : x + subdat_size[-2], y : y + subdat_size[-1]
] = subdat[channel : channel + 1, ...]

else:
ni = ceildiv(subdat_size[-2], max_load)
nj = ceildiv(subdat_size[-1], max_load)

for i in range(ni):
for j in range(nj):
print(f"\r{i+1}/{ni}, {j+1}/{nj}", end=" ")
start_x, end_x = (
i * max_load,
min((i + 1) * max_load, subdat_size[-2]),
)
start_y, end_y = (
j * max_load,
min((j + 1) * max_load, subdat_size[-1]),
)

array[
channel,
idx,
x + start_x : x + end_x,
y + start_y : y + end_y,
] = subdat[
channel : channel + 1,
start_x:end_x,
start_y:end_y,
]
print("")

# Write OME-Zarr multiscale metadata
print("Write metadata")
Expand All @@ -231,8 +229,6 @@ def convert(
multiscales[0]["axes"].insert(0, {"name": "c", "type": "channel"})

for n in range(nblevel):
shape0 = omz["0"].shape[-2:]
shape = omz[str(n)].shape[-2:]
multiscales[0]["datasets"].append({})
level = multiscales[0]["datasets"][-1]
level["path"] = str(n)
Expand All @@ -247,17 +243,17 @@ def convert(
"scale": [1.0] * has_channel
+ [
1.0,
(shape0[0] / shape[0]) * vxh,
(shape0[1] / shape[1]) * vxw,
float(2**n) * vxh,
float(2**n) * vxw,
],
},
{
"type": "translation",
"translation": [0.0] * has_channel
+ [
0.0,
(shape0[0] / shape[0] - 1) * vxh * 0.5,
(shape0[1] / shape[1] - 1) * vxw * 0.5,
float(2**n - 1) * vxh * 0.5,
float(2**n - 1) * vxw * 0.5,
],
},
]
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