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Update .zattrs file and test result #20

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merged 4 commits into from
Nov 25, 2024
Merged

Update .zattrs file and test result #20

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5c67764
Update .zattrs file
Nov 20, 2024
af4853b
Updated .zattrs scale calculation process
Nov 20, 2024
3b7b4de
style fixes by ruff
jingjingwu1225 Nov 20, 2024
a7f4d03
Update multi_slice.py
jingjingwu1225 Nov 20, 2024
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76 changes: 37 additions & 39 deletions linc_convert/modalities/df/multi_slice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def convert(
inp: list[str],
out: str | None = None,
*,
chunk: int = 4096,
chunk: int = 1024,
compressor: str = "blosc",
compressor_opt: str = "{}",
max_load: int = 16384,
Expand Down Expand Up @@ -131,7 +131,7 @@ def convert(
new_width = jp2.shape[1]
new_size = (new_height, new_width)
if has_channel:
new_size += (3.0,)
new_size += (3,)
print(len(inp), new_size, nblevel, has_channel)

# Prepare chunking options
Expand Down 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, ...][0]
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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,
][0]

print("")

# Write OME-Zarr multiscale metadata
print("Write metadata")
Expand Down
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