Comments (8)
Can you identify whether it is present in 0.1.52 and/or 0.1.53?
from tensorstore.
Both have the issue. 0.1.51 is the last version that works on my machine.
from tensorstore.
Thanks. I suspect that there's a boundary condition in c6807c4 which triggers this.
from tensorstore.
What is your downsampling for this?
from tensorstore.
Do you mean the downsample_factors
? It was [4, 4, 1, 1], and 'mean' was the downsample_method
.
from tensorstore.
We are having trouble reproducing this --- can you provide the exact steps to reproduce the issue?
from tensorstore.
here is a minimal reproducible example:
import tensorstore as ts
import cv2
src_spec = {
'driver':'neuroglancer_precomputed',
'kvstore':'gs://yuelong-test-data/tensorstore_test/W05_S001R2'
}
ds_spec = {
"driver": "downsample",
"downsample_factors": [4,4,1,1],
"downsample_method": 'mean',
"base": src_spec
}
ds_ts = ts.open(ds_spec).result()
img = ds_ts[4096:4608,4096:4608,0,0].read().result()
cv2.imwrite('test.png', img)
The source bucket was created by Michal under lcht-goog-connectomics
project, so you should have access to it. Tested on Rocky Linux 8.9 with Python 3.12.2 & Tensorstore 0.1.54.
from tensorstore.
I can verify a repro using examples/extract_slice and a downsampling of [2,2,1,1] or [4,4,1,1], with an output shape of [64, 64, 1, 1]:
SPEC='--input_spec={
"base": {
"driver": "neuroglancer_precomputed",
"kvstore": {
"bucket": "yuelong-test-data",
"driver": "gcs",
"path": "tensorstore_test/W05_S001R2/"
},
"transform": {
"input_exclusive_max": [46696, 50835, 1, 1],
"input_inclusive_min": [0, 0, 0, 0],
"input_labels": ["x", "y", "z", "channel"]
}
},
"downsample_factors": [2, 2, 1, 1],
"downsample_method": "mean",
"driver": "downsample",
"dtype": "uint8",
"transform": {
"input_exclusive_max": [4672, 4672, 1, 1],
"input_inclusive_min": [4608, 4608, 0, 0],
"input_labels": ["y", "x", "z", "channel"]
}
}'
/tmp/extract_slice.before --output_file=/tmp/before.png "${SPEC}"
/tmp/extract_slice.after --output_file=/tmp/after.png "${SPEC}"
compare -compose src /tmp/before.png /tmp/after.png /tmp/compare.png
from tensorstore.
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from tensorstore.